[English] 日本語
Yorodumi
- PDB-6v80: Crystal structure of human CD1d presenting alpha-Galactosylcerami... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v80
TitleCrystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12 TCR and VHH nanobody 1D12
Components
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
  • Nanobody VHH ID12
  • T cell receptor alpha variable 10, nkt tcr alpha chain fusion
  • nkt tcr beta chain
KeywordsIMMUNE SYSTEM / lipid / nanobody
Function / homology
Function and homology information


lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / heterotypic cell-cell adhesion / T cell receptor complex ...lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / heterotypic cell-cell adhesion / T cell receptor complex / beta-2-microglobulin binding / immune system process / detection of bacterium / positive regulation of T cell proliferation / cell adhesion molecule binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / basolateral plasma membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding
Similarity search - Function
: / : / : / MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / : / : / MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-AGH / T cell receptor alpha variable 10 / Human nkt tcr alpha chain / Human nkt tcr beta chain / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsShahine, A. / Rossjohn, J.
CitationJournal: Nat Cancer / Year: 2020
Title: A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.
Authors: Shahine, A. / Rossjohn, J.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
C: T cell receptor alpha variable 10, nkt tcr alpha chain fusion
D: nkt tcr beta chain
E: Nanobody VHH ID12
F: Antigen-presenting glycoprotein CD1d
G: Beta-2-microglobulin
H: T cell receptor alpha variable 10, nkt tcr alpha chain fusion
I: nkt tcr beta chain
J: Nanobody VHH ID12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,22716
Polymers230,21910
Non-polymers3,0086
Water00
1
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
C: T cell receptor alpha variable 10, nkt tcr alpha chain fusion
D: nkt tcr beta chain
E: Nanobody VHH ID12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3927
Polymers115,1105
Non-polymers1,2832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-68 kcal/mol
Surface area45180 Å2
MethodPISA
2
F: Antigen-presenting glycoprotein CD1d
G: Beta-2-microglobulin
H: T cell receptor alpha variable 10, nkt tcr alpha chain fusion
I: nkt tcr beta chain
J: Nanobody VHH ID12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8359
Polymers115,1105
Non-polymers1,7254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-64 kcal/mol
Surface area45560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.667, 165.250, 84.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...
21(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARG(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB34
12ASNASNASNASN(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB2122
13ILEILEMETMET(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB1 - 992 - 100
14ILEILEMETMET(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB1 - 992 - 100
15ILEILEMETMET(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB1 - 992 - 100
16ILEILEMETMET(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB1 - 992 - 100
21ARGARGARGARG(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG34
22GLNGLNASPASP(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG2 - 983 - 99
23GLNGLNASPASP(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG2 - 983 - 99
24GLNGLNASPASP(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG2 - 983 - 99
25GLNGLNASPASP(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG2 - 983 - 99

-
Components

-
Protein , 4 types, 8 molecules AFBGCHDI

#1: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 39471.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769
#3: Protein T cell receptor alpha variable 10, nkt tcr alpha chain fusion


Mass: 23365.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV10, B2M, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4J240, UniProt: K7N5M3
#4: Protein nkt tcr beta chain


Mass: 27491.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7N5M4

-
Antibody , 1 types, 2 molecules EJ

#5: Antibody Nanobody VHH ID12


Mass: 12901.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMEK219 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1

-
Sugars , 3 types, 6 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C50H99NO9
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21 % (v/v) PEG 3350, 0.2 M tri-sodium citrate, 3% (v/v) D-(+)-trehalose dehydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.39
ReflectionResolution: 3.53→82.82 Å / Num. obs: 35574 / % possible obs: 100 % / Redundancy: 15.2 % / CC1/2: 0.988 / Rpim(I) all: 0.117 / Net I/σ(I): 6
Reflection shellResolution: 3.53→3.7 Å / Redundancy: 15.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4684 / CC1/2: 0.462 / Rpim(I) all: 0.729 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PO6, 3P0G

2po6

3p0g


Resolution: 3.53→82.63 Å / Cross valid method: THROUGHOUT / σ(F): 246.34 / Phase error: 38.96 / Details: TWIN LAW: -H,-K,L
RfactorNum. reflection% reflection
Rfree0.254 1873 5.27 %
Rwork0.195 33582 -
obs0.206 35558 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 358.06 Å2 / Biso mean: 120.3 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.53→82.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14001 0 181 0 14182
Biso mean--107.33 --
Num. residues----1827
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B742X-RAY DIFFRACTIONPOSITIONAL0
12G742X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5322-3.62760.34921410.29062544268595
3.6276-3.73430.33121410.28762557269895
3.7343-3.85470.27031460.26622611275795
3.8547-3.99230.27341390.26782559269895
3.9923-4.15190.29331380.2462593273195
4.1519-4.34050.27731500.22562540269094
4.3405-4.56890.26631380.20752584272295
4.5689-4.85440.23541550.19832589274494
4.8544-5.22810.22171450.19122576272195
5.2281-5.75210.24411590.19252570272994
5.7521-6.57970.26281320.20372627275995
6.5797-8.27160.26991360.16682593272995
8.2716-35.00640.24071530.14642639279295
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6694-0.78370.87825.0119-3.23997.46890.4692-0.35050.0978-0.27480.08610.37790.58310.0576-0.47570.3243-0.0404-0.01620.5815-0.09210.794147.730317.304263.8169
24.2786-0.64092.62544.3211-2.19975.78750.38070.05720.2773-0.6718-0.34490.12571.03250.34190.06150.71760.01170.16510.45510.03191.03919.9484-8.928760.6842
35.8393-0.5625-2.67431.55270.11373.4075-0.0243-0.09690.54120.16440.12930.61810.3492-0.2966-0.06250.5727-0.0523-0.06290.57350.0711.143919.2813.251263.921
44.2323-0.87691.24233.13451.37514.1152-0.0153-0.5262-0.04180.5179-0.0606-0.27520.57070.00890.10410.4946-0.03860.00940.64090.17820.683972.017441.011268.4353
53.7065-0.9825-0.09223.73690.19724.6461-0.5524-0.25070.4686-0.21780.2137-0.0628-0.12920.11230.49850.8205-0.27680.05180.88480.01850.74188.911170.614869.4151
65.98740.90331.07185.1184-0.2276.037-0.6877-0.23391.0399-0.1982-0.173-0.3865-0.1960.01420.75060.695-0.0177-0.23290.58020.07571.048259.052451.169352.1682
71.5075-0.0785-0.36570.6334-1.05511.63250.0737-0.1710.8357-0.14330.01080.5888-0.1167-0.2078-0.10990.8383-0.1187-0.03660.577-0.14081.166681.930272.139352.6299
83.50830.67330.37941.8128-0.922.5633-0.1033-0.21720.9735-0.68670.074-0.56561.22311.1671-0.09810.60880.23630.02331.10430.2181.210477.080215.672478.5104
90.31590.0461-0.46470.08590.2130.64870.27820.06580.1758-0.5628-0.26220.54090.8921-0.56640.23910.8245-0.1687-0.15381.4079-0.09041.638615.544634.6226105.8255
105.0382-0.7853-0.54371.9537-0.42653.81990.12270.3553-0.5215-0.1961-0.1004-0.8895-0.0836-0.0697-0.00770.51990.03730.00250.47220.17531.301675.076926.6369100.8838
114.11290.86081.27915.1325-0.42823.5593-0.19511.37140.8303-0.93340.3821-0.71731.16320.6986-0.13390.89350.30690.03221.18-0.20591.031799.47062.595898.0645
125.0769-0.9544-0.38458.8432-2.04024.82810.01120.0113-0.45390.739-0.0483-0.0002-0.3177-0.2651-0.02220.3731-0.0803-0.09880.59830.07180.625165.163913.3211116.9925
133.11110.45940.16892.9429-0.93771.77940.33820.01230.0333-0.0297-0.13820.36330.42870.5327-0.17650.60540.1515-0.08510.7853-0.03071.432691.5852-0.9525114.4375
142.10370.2015-0.15342.77870.58493.72960.87910.10790.44830.2575-0.05820.1921-1.12440.1943-0.84011.0653-0.13260.18920.49520.17060.969269.812152.827590.4407
152.5535-1.0039-1.02683.6891-0.93916.13710.20850.463-0.44250.06220.39290.588-0.46-0.7233-0.4810.259-0.0084-0.03060.59480.01630.972843.319539.315106.6572
160.2335-0.5049-0.52381.18091.03490.06590.51850.246-0.95310.5079-0.85350.101-1.5761-0.65830.2530.91660.3665-0.00851.32070.20181.867214.459755.4378107.2883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 178 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 179 THROUGH 279 )A0
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 1 THROUGH 99 )B0
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 4 THROUGH 108 )C0
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 109 THROUGH 205 )C0
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 1 THROUGH 112 )D0
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 113 THROUGH 241 )D0
8X-RAY DIFFRACTION8CHAIN 'E' AND (RESID 1 THROUGH 118 )E0
9X-RAY DIFFRACTION9CHAIN 'G' AND (RESID 2 THROUGH 98 )G0
10X-RAY DIFFRACTION10CHAIN 'H' AND (RESID 4 THROUGH 114 )H0
11X-RAY DIFFRACTION11CHAIN 'H' AND (RESID 115 THROUGH 196 )H0
12X-RAY DIFFRACTION12CHAIN 'I' AND (RESID 1 THROUGH 104 )I0
13X-RAY DIFFRACTION13CHAIN 'I' AND (RESID 105 THROUGH 237 )I0
14X-RAY DIFFRACTION14CHAIN 'J' AND (RESID 1 THROUGH 119 )J0
15X-RAY DIFFRACTION15CHAIN 'F' AND (RESID 7 THROUGH 159 )F0
16X-RAY DIFFRACTION16CHAIN 'F' AND (RESID 160 THROUGH 278 )F0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more